Apologies if this has been answered elsewhere, but I've had a glance through the threads and can't see anything obvious.

I've noted that Illumina's TruSeq kits are incompatible with BS-seq at present because the polymerase mix cannot tolerate uracil. My query is how much of an issue this is to sort out? Is it just a case of finding a different Taq for the library amplification (KAPA do one that seems suitable), or does this also affect the polymerases used to conduct end-repair? What about the polymerases in the SBS chemistry? We'd be wanting to prepare these for a run on a HiScanSQ.

Publications eg http://www.ncbi.nlm.nih.gov/pubmed/19829295 generally use PhuTurboCx for the library prep PCR - as this replaces the uracils with thymidines the enzyme used in SBS, though I assume there are some tricks with basecalling etc bisulfite-seq due to the base composition imbalance - an experienced service provider should be fine with this though.